Mon Oct 10 17:03:13 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:03:13 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2671 !!! WARNING: ASL 152 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5544826 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 2.786000 54.20000 ymin,ymax (A): -30.67600 18.82300 zmin,zma (A): 50.85200 115.0560 x,y,z range (A): 51.41400 49.49900 64.20399 scale (grids/A): 0.5544826 object centre (A): 28.49300 -5.926500 82.95400 number of atom coordinates read : 2671 total number of charged atoms : 2531 net assigned charge : 4.900023 assigned positive charge : 399.7136 centred at (gu) : 89.03191 89.13991 89.46503 assigned negative charge : -394.8147 centred at (gu) : 88.93198 89.18627 89.49606 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5353 nv = 96 ne = 84 npr = 53543 no. pairs analyzed = 53543 no. exposed pairs = 3526 no. arc points = 24877 no. surface atoms = 1179 nbur = 1492 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 221 mr = 2656 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2471 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6909 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.6923246E-10 1.5639312E-10 midg,1,midg; midg,igrid,midg 9.8415009E-10 4.4820977E-11 1,midg,midg; igrid,midg,midg -5.0105592E-10 9.6621611E-10 gauss-seidel spectral radius is 0.9832032 estimated iterations to convergence 64 setup time was (sec) 0.6000000 now iterating at: 17:03:14 rms-change max change #iterations 7.5196348E-02 12.21529 at 10iterations 5.1808613E-03 0.9360962 at 20iterations 4.2583799E-04 8.2321167E-02 at 30iterations 5.8160764E-05 9.5043182E-03 at 40iterations 1.2372118E-05 2.0365715E-03 at 50iterations finished qdiffx linear iterations at : 17:03:18 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 1.2372118E-05 2.0365715E-03 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 17:03:19 4.453u 0.417s 0:06.06 80.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:03:19 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2671 !!! WARNING: ASL 152 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.663448 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 2.786000 54.20000 ymin,ymax (A): -30.67600 18.82300 zmin,zma (A): 50.85200 115.0560 x,y,z range (A): 51.41400 49.49900 64.20399 scale (grids/A): 1.663448 object centre (A): 28.49300 -5.926500 82.95400 number of atom coordinates read : 2671 total number of charged atoms : 2531 net assigned charge : 4.900023 assigned positive charge : 399.7136 centred at (gu) : 87.09489 87.41912 88.39453 assigned negative charge : -394.8147 centred at (gu) : 86.79568 87.55846 88.48810 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 58817 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24877 grid for indexing accessible points = 1.400000 m= 18915 mr = 39041 m= 2124 mr = 12858 m= 58 mr = 1008 m= 0 mr = 3 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 27004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19431 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5544826 object centre at (A) : 28.49300 -5.926500 82.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3394037E-02 2.1821316E-02 midg,1,midg; midg,igrid,midg 7.6022831E-04 -4.3419603E-04 1,midg,midg; igrid,midg,midg -7.6504261E-03 1.3149237E-03 gauss-seidel spectral radius is 0.9982174 estimated iterations to convergence 188 setup time was (sec) 0.8100000 now iterating at: 17:03:20 rms-change max change #iterations 3.254822 158.5604 at 10iterations 1.365685 58.53579 at 20iterations 0.5734699 24.34144 at 30iterations 0.2417457 9.255729 at 40iterations 0.1017837 4.509552 at 50iterations 4.2829845E-02 1.586136 at 60iterations 1.7937366E-02 0.6695185 at 70iterations 7.5718411E-03 0.2888355 at 80iterations 3.1986714E-03 0.1358414 at 90iterations 1.3514641E-03 4.8446655E-02 at 100iterations 5.7974725E-04 2.3125648E-02 at 110iterations 2.4948100E-04 1.0169983E-02 at 120iterations finished qdiffx linear iterations at : 17:03:30 total time elapsed so far: 9.950000 # loops : 120 mean,max change (kT/e) : 2.4948100E-04 1.0169983E-02 energy calculations done at 9.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.12000 DelPhi exited at 17:03:32 10.126u 0.430s 0:12.47 84.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:03:33 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2671 !!! WARNING: ASL 152 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.495172 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 2.786000 54.20000 ymin,ymax (A): -30.67600 18.82300 zmin,zma (A): 50.85200 115.0560 x,y,z range (A): 51.41400 49.49900 64.20399 scale (grids/A): 2.495172 object centre (A): 28.49300 -5.926500 82.95400 number of atom coordinates read : 2671 total number of charged atoms : 2531 net assigned charge : 4.900023 assigned positive charge : 399.7136 centred at (gu) : 85.64227 86.12850 87.59158 assigned negative charge : -394.8147 centred at (gu) : 85.19350 86.33785 87.73219 start vw surface at 0.1200000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 136615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24877 grid for indexing accessible points = 1.400000 m= 63655 mr = 96001 m= 19423 mr = 49639 m= 3386 mr = 14460 m= 230 mr = 2129 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.200000 number of dielectric boundary points 61005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 20225 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.663448 object centre at (A) : 28.49300 -5.926500 82.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2503068 0.4164710 midg,1,midg; midg,igrid,midg 3.9904143E-04 -8.3374657E-04 1,midg,midg; igrid,midg,midg -7.3680557E-02 3.3852551E-02 gauss-seidel spectral radius is 0.9991422 estimated iterations to convergence 270 setup time was (sec) 1.510000 now iterating at: 17:03:35 rms-change max change #iterations 8.399981 298.4639 at 10iterations 4.732856 156.0154 at 20iterations 2.640722 66.41711 at 30iterations 1.466269 37.90090 at 40iterations 0.8140359 21.10178 at 50iterations 0.4496402 10.12769 at 60iterations 0.2482595 5.891591 at 70iterations 0.1372979 3.037819 at 80iterations 7.5634822E-02 1.659498 at 90iterations 4.1516732E-02 0.9488096 at 100iterations 2.2903152E-02 0.5077763 at 110iterations 1.2600427E-02 0.2775884 at 120iterations 6.9307210E-03 0.1493950 at 130iterations 3.8145117E-03 9.2285156E-02 at 140iterations 2.0986113E-03 5.1418304E-02 at 150iterations 1.1522298E-03 2.4536133E-02 at 160iterations 6.3371664E-04 1.4005661E-02 at 170iterations 3.4963514E-04 7.9116821E-03 at 180iterations finished qdiffx linear iterations at : 17:03:51 total time elapsed so far: 18.19000 # loops : 180 mean,max change (kT/e) : 3.4963514E-04 7.9116821E-03 energy calculations done at 18.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.36000 DelPhi exited at 17:03:52 18.365u 0.501s 0:19.54 96.5% 0+0k 0+0io 0pf+0w